373 lines
10 KiB
Prolog
373 lines
10 KiB
Prolog
%
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% routines to manipulate distributions
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%
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:- module(clpbn_dist,
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[dist/1,
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dist/4,
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dists/1,
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dist_new_table/2,
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get_dist/4,
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get_dist_matrix/5,
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get_possibly_deterministic_dist_matrix/5,
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get_dist_domain/2,
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get_dist_domain_size/2,
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get_dist_params/2,
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get_dist_key/2,
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get_dist_all_sizes/2,
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get_evidence_position/3,
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get_evidence_from_position/3,
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dist_to_term/2,
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empty_dist/2,
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all_dist_ids/1,
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randomise_all_dists/0,
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randomise_dist/1,
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uniformise_all_dists/0,
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uniformise_dist/1,
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reset_all_dists/0,
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add_dist/6,
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additive_dists/6
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]).
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:- use_module(library(lists),
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[nth0/3,
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append/3
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]).
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:- use_module(library(clpbn),
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[use_parfactors/1]).
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:- use_module(library(matrix),
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[matrix_new/4,
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matrix_new/3,
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matrix_to_list/2,
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matrix_to_logs/1
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]).
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:- use_module(library(clpbn/matrix_cpt_utils),
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[random_CPT/2,
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uniform_CPT/2
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]).
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/*
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:- mode dist(+, -).
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:- mode get_dist(+, -, -, -).
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:- mode get_dist_params(+, -).
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:- mode get_dist_domain_size(+, -).
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:- mode get_dist_domain(+, -).
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:- mode get_dist_nparams(+, -).
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:- mode dist(?).
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:- mode dist_to_term(+,-).
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*/
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/*******************************************
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store stuff in a DB of the form:
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db(Id, Key, CPT, Type, Domain, CPTSize, DSize)
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where Id is the id,
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Key is a skeleton of the key(main functor only)
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cptsize is the table size or -1,
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DSize is the domain size,
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Type is
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tab for tabular
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avg for average
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max for maximum
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min for minimum
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trans for HMMs
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continuous
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Domain is
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a list of values
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bool for [t,f]
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aminoacids for [a,c,d,e,f,g,h,i,k,l,m,n,p,q,r,s,t,v,w,y]
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dna for [a,c,g,t]
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rna for [a,c,g,u]
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reals
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********************************************/
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:- dynamic id/1.
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id(1).
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new_id(Id) :-
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retract(id(Id)),
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Id1 is Id+1,
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assert(id(Id1)).
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reset_id :-
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retract(id(_)),
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assert(id(1)).
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dists(X) :- id(X1), X is X1-1.
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dist(V, Id, Key, Parents) :-
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dist_unbound(V, Culprit), !,
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when(Culprit, dist(V, Id, Key, Parents)).
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dist(V, Id, Key, Parents) :-
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var(Key), !,
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when(Key, dist(V, Id, Key, Parents)).
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dist(avg(Domain, Parents), avg(Domain), _, Parents).
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dist(ip(Domain, Tabs, Parents), ip(Domain,Tabs), _, Parents).
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dist(max(Domain, Parents), max(Domain), _, Parents).
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dist(min(Domain, Parents), min(Domain), _, Parents).
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dist(cons(Domain, Parent), cons(Domain), _, Parent).
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dist(p(Type, CPT), Id, Key, FParents) :-
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copy_structure(Key, Key0),
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distribution(Type, CPT, Id, Key0, [], FParents).
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dist(p(Type, CPT, Parents), Id, Key, FParents) :-
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copy_structure(Key, Key0),
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distribution(Type, CPT, Id, Key0, Parents, FParents).
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dist_unbound(V, ground(V)) :-
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var(V), !.
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dist_unbound(p(Type,_), ground(Type)) :-
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\+ ground(Type), !.
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dist_unbound(p(_,CPT), ground(CPT)) :-
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\+ ground(CPT).
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dist_unbound(p(Type,_,_), ground(Type)) :-
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\+ ground(Type), !.
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dist_unbound(p(_,CPT,_), ground(CPT)) :-
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\+ ground(CPT).
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distribution(bool, trans(CPT), Id, Key, Parents, FParents) :-
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is_list(CPT), !,
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compress_hmm_table(CPT, Parents, Tab, FParents),
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add_dist([t,f], trans, Tab, Parents, Key, Id).
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distribution(bool, CPT, Id, Key, Parents, Parents) :-
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is_list(CPT), !,
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add_dist([t,f], tab, CPT, Parents, Key, Id).
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distribution(aminoacids, trans(CPT), Id, Key, Parents, FParents) :-
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is_list(CPT), !,
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compress_hmm_table(CPT, Parents, Tab, FParents),
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add_dist([a,c,d,e,f,g,h,i,k,l,m,n,p,q,r,s,t,v,w,y], trans, Tab, FParents, Key, Id).
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distribution(aminoacids, CPT, Id, Key, Parents, Parents) :-
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is_list(CPT), !,
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add_dist([a,c,d,e,f,g,h,i,k,l,m,n,p,q,r,s,t,v,w,y], tab, CPT, Parents, Key, Id).
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distribution(dna, trans(CPT), Key, Id, Parents, FParents) :-
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is_list(CPT), !,
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compress_hmm_table(CPT, Parents, Tab, FParents),
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add_dist([a,c,g,t], trans, Tab, FParents, Key, Id).
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distribution(dna, CPT, Id, Key, Parents, Parents) :-
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is_list(CPT), !,
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add_dist([a,c,g,t], tab, CPT, Key, Id).
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distribution(rna, trans(CPT), Id, Key, Parents, FParents) :-
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is_list(CPT), !,
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compress_hmm_table(CPT, Parents, Tab, FParents, FParents),
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add_dist([a,c,g,u], trans, Tab, Key, Id).
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distribution(rna, CPT, Id, Key, Parents, Parents) :-
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is_list(CPT), !,
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add_dist([a,c,g,u], tab, CPT, Parents, Key, Id).
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distribution(Domain, trans(CPT), Id, Key, Parents, FParents) :-
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is_list(Domain),
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is_list(CPT), !,
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compress_hmm_table(CPT, Parents, Tab, FParents),
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add_dist(Domain, trans, Tab, FParents, Key, Id).
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distribution(Domain, CPT, Id, Key, Parents, Parents) :-
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is_list(Domain),
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is_list(CPT), !,
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add_dist(Domain, tab, CPT, Parents, Key, Id).
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add_dist(Domain, Type, CPT, _, Key, Id) :-
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recorded(clpbn_dist_db, db(Id, Key, CPT, Type, Domain, _, _), _), !.
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add_dist(Domain, Type, CPT, Parents, Key, Id) :-
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length(CPT, CPTSize),
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length(Domain, DSize),
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new_id(Id),
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find_parent_sizes(Parents, Id, PSizes, [DSize|PSizes]),
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recordz(clpbn_dist_db,db(Id, Key, CPT, Type, Domain, CPTSize, DSize),_).
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find_parent_sizes([], Id, [], DSizes) :-
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recordz(clpbn_dist_psizes,db(Id, DSizes),_).
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find_parent_sizes([P|Parents], Id, [Size|Sizes], DSizes) :-
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integer(P), !,
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Size = P,
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find_parent_sizes(Parents, Id, Sizes, DSizes).
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find_parent_sizes([P|Parents], Id, [Size|Sizes], DSizes) :-
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clpbn:get_atts(P,dist(Dist,_)), !,
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get_dist_domain_size(Dist, Size),
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find_parent_sizes(Parents, Id, Sizes, DSizes).
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find_parent_sizes([_|_], _, _, _).
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%
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% Often, * is used to code empty in HMMs.
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%
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compress_hmm_table([], [], [], []).
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compress_hmm_table([*|L],[_|Parents],NL,NParents) :- !,
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compress_hmm_table(L,Parents,NL,NParents).
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compress_hmm_table([Prob|L],[P|Parents],[Prob|NL],[P|NParents]) :-
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compress_hmm_table(L,Parents,NL,NParents).
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dist(Id) :-
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recorded(clpbn_dist_db, db(Id, _, _, _, _, _, _), _).
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get_dist(Id, Type, Domain, Tab) :-
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recorded(clpbn_dist_db, db(Id, _, Tab, Type, Domain, _, _), _).
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get_dist_matrix(Id, Parents, Type, Domain, Mat) :-
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recorded(clpbn_dist_db, db(Id, _, Tab, Type, Domain, _, DomainSize), _),
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get_dsizes(Parents, Sizes, []),
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matrix_new(floats, [DomainSize|Sizes], Tab, Mat),
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matrix_to_logs(Mat).
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get_possibly_deterministic_dist_matrix(Id, Parents, Type, Domain, Mat) :-
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recorded(clpbn_dist_db, db(Id, _, Tab, Type, Domain, _, DomainSize), _),
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get_dsizes(Parents, Sizes, []),
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matrix_new(floats, [DomainSize|Sizes], Tab, Mat).
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get_dsizes([], Sizes, Sizes).
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get_dsizes([P|Parents], [Sz|Sizes], Sizes0) :-
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clpbn:get_atts(P,dist(Dist,_)),
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get_dist_domain_size(Dist, Sz),
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get_dsizes(Parents, Sizes, Sizes0).
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get_dist_params(Id, Parms) :-
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recorded(clpbn_dist_db, db(Id, _, Parms, _, _, _, _), _).
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get_dist_all_sizes(Id, DSizes) :-
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recorded(clpbn_dist_psizes,db(Id, DSizes),_).
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get_dist_domain_size(DistId, DSize) :-
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use_parfactors(on), !,
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pfl:get_pfl_parameters(DistId, _, Dist),
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length(Dist, DSize).
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get_dist_domain_size(avg(D,_), DSize) :- !,
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length(D, DSize).
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get_dist_domain_size(ip(D,_,_), DSize) :- !,
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length(D, DSize).
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get_dist_domain_size(Id, DSize) :-
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recorded(clpbn_dist_db, db(Id, _, _, _, _, _, DSize), _).
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get_dist_domain(Id, Domain) :-
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recorded(clpbn_dist_db, db(Id, _, _, _, Domain, _, _), _), !.
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get_dist_domain(avg(Domain), Domain).
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get_dist_key(Id, Key) :-
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use_parfactors(on), !,
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pfl:get_first_pvariable(Id, Key).
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get_dist_key(Id, Key) :-
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recorded(clpbn_dist_db, db(Id, Key, _, _, _, _, _), _).
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get_dist_nparams(Id, NParms) :-
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recorded(clpbn_dist_db, db(Id, _, _, _, _, NParms, _), _).
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get_evidence_position(El, ip(Domain,_,_), Pos) :- !,
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nth0(Pos, Domain, El), !.
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get_evidence_position(El, avg(Domain), Pos) :- !,
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nth0(Pos, Domain, El), !.
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get_evidence_position(El, Id, Pos) :-
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recorded(clpbn_dist_db, db(Id, _, _, _, Domain, _, _), _),
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nth0(Pos, Domain, El), !.
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get_evidence_position(El, Id, Pos) :-
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recorded(clpbn_dist_db, db(Id, _, _, _, _, _, _), _), !,
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throw(error(domain_error(evidence,Id),get_evidence_position(El, Id, Pos))).
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get_evidence_position(El, Id, Pos) :-
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throw(error(domain_error(no_distribution,Id),get_evidence_position(El, Id, Pos))).
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get_evidence_from_position(El, Id, Pos) :-
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recorded(clpbn_dist_db, db(Id, _, _, _, Domain, _, _), _),
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nth0(Pos, Domain, El), !.
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get_evidence_from_position(El, Id, Pos) :-
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recorded(clpbn_dist_db, db(Id, _, _, _, _, _, _), _), !,
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throw(error(domain_error(evidence,Id),get_evidence_from_position(El, Id, Pos))).
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get_evidence_from_position(El, Id, Pos) :-
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throw(error(domain_error(no_distribution,Id),get_evidence_from_position(El, Id, Pos))).
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dist_to_term(_Id,_Term).
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empty_dist(Dist, TAB) :-
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use_parfactors(on), !,
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pfl:get_pfl_factor_sizes(Dist, DSizes),
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matrix_new(floats, DSizes, TAB).
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empty_dist(Dist, TAB) :-
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recorded(clpbn_dist_psizes,db(Dist, DSizes),_), !,
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matrix_new(floats, DSizes, TAB).
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empty_dist(Dist, TAB) :-
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throw(error(domain_error(no_distribution,Dist),empty_dist(Dist,TAB))).
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dist_new_table(DistId, NewMat) :-
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use_parfactors(on), !,
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matrix_to_list(NewMat, List),
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pfl:new_pfl_parameters(DistId, _, List).
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dist_new_table(Id, NewMat) :-
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matrix_to_list(NewMat, List),
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recorded(clpbn_dist_db, db(Id, Key, _, A, B, C, D), R),
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erase(R),
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recorda(clpbn_dist_db, db(Id, Key, List, A, B, C, D), _),
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fail.
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dist_new_table(_, _).
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copy_structure(V, _) :- attvar(V), !.
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copy_structure(V, V) :- var(V), !.
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copy_structure(V, _) :- primitive(V), !.
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copy_structure(Key, Key0) :-
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Key =.. [A|LKey],
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copy_Lstructure(LKey, LKey0),
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Key0 =.. [A|LKey0].
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copy_Lstructure([], []).
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copy_Lstructure([H|LKey], [NH|LKey0]) :-
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copy_structure(H, NH),
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copy_Lstructure(LKey, LKey0).
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randomise_all_dists :-
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randomise_dist(_),
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fail.
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randomise_all_dists.
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randomise_dist(Dist) :-
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(
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use_parfactors(on)
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->
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pfl:get_pfl_factor_sizes(Dist, DSizes)
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;
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recorded(clpbn_dist_psizes, db(Dist,DSizes), _)
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),
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random_CPT(DSizes, NewCPT),
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dist_new_table(Dist, NewCPT).
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uniformise_all_dists :-
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uniformise_dist(_),
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fail.
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uniformise_all_dists.
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uniformise_dist(Dist) :-
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(
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use_parfactors(on)
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->
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pfl:get_pfl_factor_sizes(Dist, DSizes)
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;
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recorded(clpbn_dist_psizes, db(Dist,DSizes), _)
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),
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uniform_CPT(DSizes, NewCPT),
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dist_new_table(Dist, NewCPT).
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reset_all_dists :-
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recorded(clpbn_dist_psizes, _, R),
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erase(R),
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fail.
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reset_all_dists :-
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recorded(clpbn_dist_db, _, R),
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erase(R),
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fail.
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reset_all_dists :-
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reset_id,
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fail.
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reset_all_dists.
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additive_dists(ip(Domain,Tabs1), ip(Domain,Tabs2), Parents1, Parents2, ip(Domain,Tabs), Parents) :-
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append(Tabs1, Tabs2, Tabs),
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append(Parents1, Parents2, Parents).
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